Total-Evidence Dating under the Fossilized Birth–Death Process

Abstract

Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth–death (FBD) process, which has been used to model speciation, extinction, and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of data sets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants, and bees). Previous total-evidence dating analyses of this data set were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push toward more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed.

Inferring node dates from tip dates in fossil Canidae: the importance of tree priors

“…If, however, strongly informative priors on rates or node age calibrations are required to produce reasonable results under the uniform tree prior, its main appeal is lost. The addition of BDSS/FBD models with SAs to MRBAYES [5] suggests that the best prospects for tip-dating may lay in adding realism to mechanistic models, rather than in attempting to devise non-mechanistic, agnostic dating priors.…”

“…Canidae are unusually well sampled. In other cases, researchers may only have a handful of fossils when true diversity was hundreds or thousands of species (closer to the situation in the exemplar Hymenoptera dataset explored by [3,5]). In such situations, the uniform tree prior's performance may improve relative to BDSS-type models attempting to estimate mechanistic parameters from few data.…”

“…These models can be categorized broadly into two types: mechanistic models where trees are a function of parametrized speciation, extinction and sampling processes, termed birth-death-serial-sampling (BDSS; [1]) or fossilized birth-death (FBD; [2]) models, and the non-mechanistic uniform, prior on trees and node ages [3], which does not have parameters for the rates of these processes. BDSS/FBD models can allow or disallow sampled ancestors (SAs; [4,5]). Importantly, tip-dating methods allow researchers to avoid relying on node calibrations.…”

Five palaeobiological laws needed to understand the evolution of the living biota

“…Thus, the preponderance of molecular analyses that yield zero extinction rates, or extinction rates that are a small fraction of the origination rate are almost certainly inaccurate, especially when one reflects on the fact that zero or low extinction translates into exponential growth, which is just as unlikely at the species level as it is at the population level. In light of the third law, we need to test the methods for deriving extinction rates from molecular phylogenies against rates measured in the fossil record, and continue developing methods that integrate molecular phylogenetic and fossil data in dating molecular phylogenies, such as the fossilized birth-death process 34 and total evidence dating 35 , to provide better estimates of origination and extinction rates. Critically, we need to bear in mind the possibility that phylogenetic data from only living taxa might simply be insufficient to reliably infer past origination and extinction rates 36 .…”

Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata)

“…I encourage readers to refer to these references for additional details on birth-death sampling models and their applications. Interested readers are also encouraged to see Gavryushkina et al (2014) and Zhang et al (2016) for a detailed description of a birth-death sampling process with time heterogeneous (i.e., piecewise-constant) rates, as well as Bapst's (2013) probabilistic method to a posteriori timescale undated cladograms. Please note that the notation used in this paper differs in places from that of the references mentioned above to be more consistent with the paleontological literature (e.g., Foote, 1997Foote, , 2000Wagner and Marcot, 2010;Bapst, 2012).…”